(1) Experiments that describe the state of something in the cell under defined conditions. A datum derived from these experiments is called a SDatum (for state datum).

(2) Experiments that describe the change in the state of something in the cell when the defined conditions are altered. A datum derived from this kind of experiment is called a CDatum (for change datum).

The structure of a datum

The first line of a datum

A "basic" experiment:

A system is defined in regards to a testable parameter (SDatum)

The system is perturbed and the effect on the testable parameter is determined. (CDatum)

An experiment with "extras":

A change is made to the basic experiment and the change in the effect of the testable parameter is determined.

The first line of the datum supplies information about the basic experiment.

Format for CDatums: Subject Assay Change Treatment (times)

Format for SDatums: Subject Assay Detectablility

The cells line describes the cells and the medium/conditions used in the basic experiment. Any attributes such as expressed or knocked-out proteins not mentioned on the first line are listed here.

The times line supplies additional information about the times studied and the relative change (if any) in the reponse.

The IPfrom line supplies information about the source of an immunoprecipitate used in a test-tube experiment. If more than one immunoprecipitate are used in an experiment they are numbered (e.g IP1from and IP2from).

The extras describe changes made to the basic experiment and the influence the changes have on the results.

The source line supplies the PubMed ID of the reference and the figure or table that displays the data.

The comments line provides information not mentioned in the other lines.

In Pathway Logic genes use the Protein name followed by -gene. Genes do not have prefixes, mutations, or modifications. They do not require handles because they are easily identified by their sequences.

The Cell Lines section also contains ATCC catalog numbers if available, synonyms, growth conditions, molecular charactistics, and references. This information is by no means complete - but it has been used as a repository of information about the cell lines picked up during curation.

Primary Cells:

Primary Cells are given names based on the species and tissues from which they were derived and the purification methods used.

In some experiments, the cells used can not be categorized as cell lines or primary cells. In those case, the contents of the cells line is surrounded by quote marks. This is a cue to the datum parser to treat the contents as a string. It is a cue to the reader that the derivation of the cells is not described in this manual and that the reader has to hunt down the details from the original source.

examples:

cells: "disaggregated embryonic day-12.5 mouse embryos"

In this example, the entire mouse embryo is disaggregated into cells but the cells are not cultured before use.

cells: "mSCs + mLNCs in BMS activated with anti-Cd3 for 48 hr"

In this example, cells from both the mouse spleens and lymph nodes are mixed.

attributes:

<Protein-null> cell does not contain endogenous protein

<xProtein> cells has been transfected (either stable or transiently) with a plasmid that expresses Protein.

<xProtein(mutation)> cells has been transfected (either stable or transiently) with a plasmid that expresses Protein containing a mutation.

Medium:

BMHIS: basal medium containing heat-inactivated serum

BMLS: basal medium containing low serum

used when cells are "serum-starved" or in less than 2% serum or "made quiescent"

BMS: basal medium containing serum

eg "growth medium"

note: BMS is used if no description of the medium is given

BSS: balanced salt solution

MNR: medium not reported

other-stuff:

any conditions that are common to all the samples in the experiment

The times Line:

This line shows the time points measured and the relative change in the response.

The response is shown by using "+" after each time point. The number of "+"s used does not represent the size or intensity of the response, only the change in the size or intensity of the response.

Response times less than 1 min are not collected.

examples:

times: 0 5++ 15+ 60 min

In this example, the initial signal is undetectable. The peak response is at 5 min. The signal is decreased by 15 min and undetectable at 60 min.

times: 0++ 30+ 60 120 240+ min

In this example, the initial signal is detectable. The signal decreases at 30 min and is no longer detectable at 60 min. The signal returns at 240 min but is not as strong as the initial signal.

times: 0 1 3+ 5+ 15+ 30+ 60+ min

In this example, the initial signal is undetectable. The signal is detectable by 3 min and stays detectable for up to 60 min.

Extras:

Each extra line contains a refinement of the basic experiment that provides additional information about the influence of various parameters on the outcome. These include:

The effect of the removal of a Protein or Proteins for a response to occur is is demonstrated by performing the basic the experiment using:

a positive change or detectability is unchanged by addition of a Ligand, anti-Receptor antibody, stress, or nutrient to the basic experiment

a chemical may be a stimulus if it produces a known response

The source Line:

source: PMID-Fig-## or source: PMID-Table-##

examples:

source: 9094716-Fig-2d

source: 9094716-Fig-2e,3b,3e,4c,4d

source: 9020886-Table-1,Fig-3

If the same experiement is done twice, more than figure or table numbers can be used

In some cases, attempts were made to consolidate similar experiments in one datum. This was not a good idea and is in the process of being undone.

source: PMID(D)

example:

source: 14633987(D)

This is left over from the days when we tried to make rules from review papers as well as "data" papers. The (D) was used to designate the source as a paper containing data and (R) was used to designate the source as a review or commentary. We are in the process of replacing (D) with figure numbers.